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NC_000913.2.gbk- reference genome for a related (but not identical) strain.singlepairedc20.fa
Be sure to add them in this order! We need the reference first.
To remind you of what we are looking at:
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NC_000913.2.gbksingle.fapairedc20.fapairedc25.fapairedc50.fa
Warning! single.fa has a lot of sequences. If you add it to the mix, things will get ugly.
Transferring annotation
Mauve has a useful feature to transfer the coordinates of genes across the alignment that it has made by Move Contigs. This can be a good way of assigning orthologs.
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- Circos - fully featured. Very cool functions for drawing connections between different chromosome locations.
- CGView Simpler to use. Better functionality for showing genes up close as arrows. Does not draw links.
Evaluating eukaryotic assemblies
If you are going to seriously annotate a eukaryotic genome, then you are going to need a machine with database infrastructure and other tools installed. Here are two systems for annotating gene structure in eukaryotic genomes as examples:
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